[Bioperl-l] GO annotatinos in BioPerl. A tentative proposal...

Jeffrey Chang jchang@SMI.Stanford.EDU
Thu, 5 Apr 2001 18:25:07 -0700 (PDT)

On Thu, 5 Apr 2001, Mark Wilkinson wrote:

> > > At 04:17 PM 4/5/2001 , Jeffrey Chang wrote:
> > > >I urge you to keep the representation of GO separate from the annotation
> > > >on the sequence.  The sequence should contain only a very minimal
> > > >reference to an annotation, possibly as a perl pointer or a GO ID.


> I would, on the contrary, strongly disagree that a sequence feature is
> not the place to hang the annotation of that feature... or am I
> misunderstanding you? Certainly, speaking as an annotator, the *last*
> thing I need is to have access to only a minimally annotated sequence.  
> I need my sequence/feature objects to be loaded with as much
> annotation as is available so that I can evaluate it.

No, nothing about minimally annotated sequences.  I am arguing that the
SeqFeature and Annotation objects should not contain the structure of the
annotation.  That is, those objects should only contain the minimum amount
of information necessary to uniquely identify a GO code (e.g. GO ID), and
the structure of GO (IS-A and PART-OF relationships) should be maintained
separately in a different set of objects.